As a bit of a subway geek, this article in the Times about selling corporate naming rights to the Atlantic Avenue station got me thinking: What other stations, through quirks of history, actually have commercial names, even if we don't realize it? For the purposes of this exercise, non-profit entities (like Columbia or the Museum of Natural History) don't count, though no-longer-existent commercial entities do. Fact checked using Wikipedia, the Encyclopedia of New York City, nycsubway.org and Forgotten New York.
Train stations
There are two subway stations that are part of old railway stations, each of which is named for the railroad company that built them. Penn Station is, of course, named after the Pennsylvania Railroad Company, a fact which makes possible the elocutively bewildering experience of going from New York Penn Station to Newark Penn Station. Grand Central-42nd Street gets its name from Grand Central Terminal, which gets its name in turn from the New York Central Railroad of Vanderbilt fame.
Newspaper squares
When Adolph Ochs moved his newspaper to Longacre Square in 1904, he got the city to rename the area Times Square, a name that has been retained even though the Times hasn't actually been on the square since 1913. I would speculate that the cost of redoing all of the name plates in the Times Square-42nd Street station had something to do with it.
Herald Square was named after the New York Herald, which was headquartered there from 1893 to sometime in the 1920s. I want to say that the city renamed the square after the success of Times Square in a successful attempt to get the Herald to move there, but I can't find any references to back me up on that story at the moment.
Sports stadiums
An interesting thing to note about Barclay's purchase is that it's consistent with MTA practices of the past in naming stations after professional sports venues. Prior to this year, both baseball stadiums in New York City had their names on their respective subway stops, though it does not appear to be the case that Ebbets Field was so lucky (actually, looking at some old maps it looks like Yankee Stadium wasn't so lucky at the time either).
However, when the name of Shea Stadium's replacement was announced, the MTA balked at the idea of putting the name of a giant bank on the wall without being compensated, an idea I applauded. A beleaguered Citibank failed to pony up, and the Mets-Willets Point station was born. 161 Street-Yankee Stadium remained of course.
For some reason, while posting the trademarks of corporate sponsors requires payment, the MTA is fine with the trademarks of the teams themselves. Both team names are trademarks; whether those marks are registered to the team owners or to MLB is unclear to me.
Other commercial place names
63rd Drive on the R and V trains (the IND Queens Boulevard line) has the subtitle Rego Park, a neighborhood named after the Real Good Construction company, which built it. On the same line is Steinway Street. Including that station on this list is a bit of a stretch, because it seems as if the street is named after Steinway the man who owned the piano company that dominated the neighborhood to the north and not the piano company itself.
Are there any that I missed?